Iva Veseli of anvi'o
Bio
Computer scientist and biologist who leverages computational methods to study microbial metabolism in environmental metagenomes.
Affiliations
currentPost-doctoral Scientist, Helmholtz Institute for Functional Marine Biodiversity at OldenburgpastGraduate Student, The Biophysical Sciences Program at the University of ChicagopastFellow, NSF Graduate Research Fellowship Program
Contact info or affiliations needs an update? Edit these files.
Intellectual contributions
Some contributions are more than code. Inevitably, this manually curated list will be incomplete for almost everyone, but nevertheless, we try to keep track of key contributions made by memebers of the anvi'o commmunity to the platform and its users. Edit these files to help.
- Spearheaded the development of anvi'o metabolism framework.
- Spearheaded the 'omics vocabulary effort.
Program contributions
anvi-compute-functional-enrichment-across-genomes anvi-compute-functional-enrichment-in-pan anvi-compute-metabolic-enrichment anvi-display-metabolism anvi-estimate-metabolism anvi-migrate anvi-run-hmms anvi-run-kegg-kofams anvi-run-pfams anvi-setup-kegg-data anvi-setup-pfams anvi-setup-user-modules anvi-summarize-blitz anvi-script-estimate-metabolic-independence anvi-script-gen-genomes-file anvi-script-gen-user-module-file
Resource contributions
Tutorials and exercises
Kinds of write-ups that typically use mock or simple datasets to describe basic concepts and how to accomplish common tasks in anvi'o often with hands-on experience.
A hands-on exercise for the metabolism suite of programs in anvi’o. It starts with a section on how to estimate metabolism for a single bacterial isolate, and goes into larger, real-world dataset of metagenome-assembled genomes to demonstrate how to estimate metabolism compute enrichment scores for metabolic modules.
A tutorial that walks you through some of the most fundamental aspects of anvi'o and its application to a real-world dataset organized in multiple interconnected chapters, which all use the same dataset.
Materials from a 2022 workshop on metagenomics in anvi'o, including read recruitment and metabolism estimation.
Materials and a tutorial from the 2023 iteration of our metagenomics workshop.
Technical write-ups
Solutions or discussions regarding matters that are typically more technical than scientific.
A resource that describes how to find anvi'o programs and understand their utility, how to reach out to anvi'o community, and how to report technical problems.
Articles, workflows, opinions
Key insights into specific topics and can be useful to more advanced users and 'omics enthusiasts in general.
The pitfalls of bioinformatics software development and the beauty of open-source code.
Using metabolism estimation to go fishing in some ocean metagenomes.
Showcasing our strategy for consolidating and sharing data with a C-CoMP model organism.